I am able to reproduce this locally
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'uncoverappLib-Ex.R' failed
The error most likely occurred in:
> ### Name: buildInput
> ### Title: Build input file
> ### Aliases: buildInput
>
> ### ** Examples
>
> gene.list<- system.file("extdata", "mygene.txt", package = "uncoverappLib")
>
> bam_example <- system.file("extdata", "example_POLG.bam",
+ package = "uncoverappLib")
> cat(bam_example, file = "bam.list", sep = "\n")
> temp_dir=tempdir()
> buildInput(geneList= gene.list, genome= "hg19", type_bam= "chr",
+ bamList= "bam.list",type_input="genes", outDir= temp_dir)
Reading gene name started at:
2022-11-10 12:53:21.140608
Read 1 item
'select()' returned 1:many mapping between keys and columns
Error in buildInput(geneList = gene.list, genome = "hg19", type_bam = "chr", :
ERROR: unrecognized GENE NAME. Please remove genes
stored in preprocessing_log1.txt
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ...
What version of R and Bioc are you using to test?
You should be using R 4.2.2 and Bioc 3.16
Have you run a BiocManager::install() and BiocManager::valid() to ensure you
are using the latest versions of all packages?
Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Emanuela
Iovino <emanuela.iov...@unibo.it>
Sent: Tuesday, November 8, 2022 8:42 AM
To: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: [Bioc-devel] R: uncoverappLib problems reported in the Multiple
platform build/check report for BioC 3.16
Hi,
I keep getting to receive an error in my package during check process, I tried
to reproduce the error in my environment, but I cannot understand what it is
going wrong, because
devtools::check() and BiocCheck do not return any error, I guess that
something's wrong in a file stored as example (mygene.txt) and despite I have
modified it I receive the same error. Could you please help me to handle this?
Thanks
________________________________
Da: bbs-nore...@bioconductor.org <bbs-nore...@bioconductor.org>
Inviato: luned� novembre 2022 18:00
A: Emanuela Iovino <emanuela.iov...@unibo.it>
Oggetto: uncoverappLib problems reported in the Multiple platform build/check
report for BioC 3.16
[This is an automatically generated email. Please don't reply.]
Hi uncoverappLib maintainer,
According to the Multiple platform build/check report for BioC 3.16,
the uncoverappLib package has the following problem(s):
o ERROR for 'R CMD check' on nebbiolo2. See the details here:
https://secure-web.cisco.com/1ye23e6VILCo8EGm_FZohksBP40u7sJ3WQpoPakwn0933iJny1qcPU7XRyU6P0dZnVrboE-a-vAnunNzohAlhsTPQ4nLnNVREHlrN2OrleZFQtDXV8x89Xc75R-sbHaEtaDT05samq7NVk8rwhF3zxdSA0gh2JkktsHmP2TllJPXGUmBD70gR-FPvSP46-Im5qOExaUKiesueZ2fFJbnnPaGVtAn9yl4nu7_WlJ7eGYQFZRW8219icQjwb5QLkQLvimXYCBrKrSuLonVGPHzXujRWJwhnSVDEAmEthQPbpssmWrriWihf2Gd10CMTIDRV/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.16%2Fbioc-LATEST%2FuncoverappLib%2Fnebbiolo2-checksrc.html
Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org
Notes:
* This was the status of your package at the time this email was sent to you.
Given that the online report is updated daily (in normal conditions) you
could see something different when you visit the URL(s) above, especially if
you do so several days after you received this email.
* It is possible that the problems reported in this report are false
positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.
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